FORMOSAT-5 consists of a spacecraft bus and an electro-optical payload. The payload is an f/8 Cassegrain type telescope with 3.6-m effective focal length. The spacecraft has a ground sampling distance of 2-m for panchromatic and 4-m for multispectral bands, with a 24-km swath width. FORMOSAT-5 is the first space program that National Space Organization (NSPO) takes full responsibility for the complete satellite and payload system engineering. The optical system assembly (OSA) has been successfully aligned and is now undergoing final performance verification tests at system level. To help create this unique instrument, NSPO has developed the computer aided alignment method assisted with the mechanical ground support equipment to carry out the assembly, alignment, and verification of the complex systems. This method offers an integrated capability for interferometric alignment and characterization of the large instrument. A detail OSA integration and verification steps, including primary mirror, secondary mirror, corrector lens and baffles alignment are presented. This paper describes the overall capability of this method and uses decomposed Zernike polynomials from the alignment and characterization of the OSA to verify the reduction of the wavefront errors and misalignments. It further demonstrates the successful completion of the instrument and satisfaction with the main system requirements.